Bacterial and plant ketol-acid reductoisomerases have different mechanisms of induced fit during the catalytic cycle

Journal of Molecular Biology

Volumn 424, Issue 3-4, 2012, Pages 168-179

  Wong, Sze Ho ^a   Lonhienne, Thierry G A ^a   Winzor, Donald J ^a   Schenk, Gerhard ^a,b   Guddat, Luke W ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

antibacterial; branched chain amino acid biosynthesis; conformational change; KARI; X ray crystallography

Indexed keywords

KETOL ACID REDUCTOISOMERASE; MAGNESIUM ION; POLYPEPTIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME STABILITY; ENZYME STRUCTURE; ESCHERICHIA COLI; ISOTHERMAL TITRATION CALORIMETRY; PRIORITY JOURNAL; PROTEIN FOLDING; SALMONELLA TYPHIMURIUM; SEDIMENTATION; STOICHIOMETRY; ULTRACENTRIFUGATION;

ANIMALIA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; FUNGI;

EID: 84869084004     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.09.018     Document Type: Article

References (32)

1. G. Levitt, H.L. Ploeg, R.C. Weigel, and D.J. Fitzgerald 2-Chloro-N-[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)aminocarbonyl] benzenesulfonamide, a new herbicide J. Agric. Food Chem. 29 1981 416 418
2. R.A. Boigegrain, J.P. Liautard, and S. Kohler Targeting of the virulence factor acetohydroxyacid synthase by sulfonylureas results in inhibition of intramacrophagic multiplication of Brucella suis Antimicrob. Agents Chemother. 49 2005 3922 3925 (Pubitemid 41233051)
3. K.J. Choi, Y.G. Yu, H.G. Hahn, J.D. Choi, and M.Y. Yoon Characterization of acetohydroxyacid synthase from Mycobacterium tuberculosis and the identification of its new inhibitor from the screening of a chemical library FEBS Lett. 579 2005 4903 4910
4. A. Aulabaugh, and J.V. Schloss Oxalyl hydroxamates as reaction-intermediate analogs for ketol-acid reductoisomerase Biochemistry 29 1990 2824 2830 (Pubitemid 20122618)
5. A. Schulz, P. Sponemann, H. Kocher, and F. Wengenmayer The herbicidally active experimental compound Hoe-704 is a potent inhibitor of the enzyme acetolactate reductoisomerase FEBS Lett. 238 1988 375 378
6. J.A. Grandoni, P.T. Marta, and J.V. Schloss Inhibitors of branched-chain amino acid biosynthesis as potential antituberculosis agents J. Antimicrob. Chemother. 42 1998 475 482 (Pubitemid 28473007)
7. R. Dumas, C. Cornillon-Bertrand, P. Guigue-Talet, P. Genix, R. Douce, and D. Job Interactions of plant acetohydroxy acid isomeroreductase with reaction intermediate analogues: correlation of the slow, competitive, inhibition kinetics of enzyme activity and herbicidal effects Biochem. J. 301 Pt 3 1994 813 820 (Pubitemid 24239317)
8. R. Tyagi, Y.T. Lee, L.W. Guddat, and R.G. Duggleby Probing the mechanism of the bifunctional enzyme ketol-acid reductoisomerase by site-directed mutagenesis of the active site FEBS J. 272 2005 593 602
9. S.K. Chunduru, G.T. Mrachko, and K.C. Calvo Mechanism of ketol acid reductoisomerase - steady-state analysis and metal-ion requirement Biochemistry 28 1989 486 493
10. H.J. Ahn, S.J. Eom, H.J. Yoon, B.I. Lee, H.J. Cho, and S.W. Suh Crystal structure of class I acetohydroxy acid isomeroreductase from Pseudomonas aeruginosa J. Mol. Biol. 328 2003 505 515 (Pubitemid 36407590)
11. V. Biou, R. Dumas, C. Cohen-Addad, R. Douce, D. Job, and E. Pebay-Peyroula The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 Å resolution EMBO J. 16 1997 3405 3415 (Pubitemid 27250036)
12. K. Thomazeau, R. Dumas, F. Halgand, E. Forest, R. Douce, and V. Biou Structure of spinach acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxymethylvalerate, manganese and (phospho)-ADP-ribose Acta Crystallogr., Sect. D: Biol. Crystallogr. 56 2000 389 397 (Pubitemid 30231218)
13. 2 + and NADPH binding as revealed by two crystal structures J. Mol. Biol. 389 2009 167 182
14. 2 + ions, NADPH, and a competitive inhibitor Biochemistry 38 1999 6025 6034
15. R. Tyagi, S. Duquerroy, J. Navaza, L.W. Guddat, and R.G. Duggleby The crystal structure of a bacterial class II ketol-acid reductolsomerase: domain conservation and evolution Protein Sci. 14 2005 3089 3100 (Pubitemid 41770149)
16. K.E. Vanholde, and R.L. Baldwin Rapid attainment of sedimentation equilibrium J. Phys. Chem. 62 1958 734 743
17. S.M. Arfin, and H.E. Umbarger Purification and properties of acetohydroxy acid isomeroreductase of Salmonella typhimurium J. Biol. Chem. 244 1969 1118 1127
18. Y.T. Lee, H.T. Ta, and R.G. Duggleby Cyclopropane-1,1-dicarboxylate is a slow-, tight-binding inhibitor of rice ketol-acid reductoisomerase Plant Sci. 168 2005 1035 1040 (Pubitemid 40263394)
19. J.D. Thompson, D.G. Higgins, and T.J. Gibson Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680 (Pubitemid 24354800)
20. S.T. Rao, and M.G. Rossmann Comparison of super-secondary structures in proteins J. Mol. Biol. 76 1973 241 256
21. L. Hong, and B.M. Goldstein Carboxamide group conformation in the nicotinamide and thiazole-4-carboxamide rings: implications for enzyme binding J. Med. Chem. 35 1992 3560 3567
22. P.K. Smith, R.I. Krohn, G.T. Hermanson, A.K. Mallia, F.H. Gartner, and M.D. Provenzano Measurement of protein using bicinchoninic acid Anal. Biochem. 150 1985 76 85 (Pubitemid 16258399)
23. T.M. McPhillips, S.E. McPhillips, H.J. Chiu, A.E. Cohen, A.M. Deacon, and P.J. Ellis Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines J. Synchrotron Radiat. 9 2002 401 406
24. Z. Otwinowski, and W. Minor Processing of X-ray Diffraction Data Collected in Oscillation Mode Macromolecular Crystallography, Part A 276 1997 Academic Press San Diego, CA
25. A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallogr. 30 1997 1022 1025 (Pubitemid 127485985)
26. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr., Sect. D: Biol. Crystallogr. 53 1997 240 255 (Pubitemid 27235885)
27. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, and N. Echols PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 66 2010 213 221
28. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
29. V.B. Chen, W.B. Arendall, J.J. Headd, D.A. Keedy, R.M. Immormino, and G.J. Kapral MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 66 2010 12 21
30. W.L. DeLano Use of PYMOL as a communications tool for molecular science Abstr. Pap. Am. Chem. Soc. 228 2004 U313 U314
31. L. Potterton, S. McNicholas, E. Krissinel, J. Gruber, K. Cowtan, and P. Emsley Developments in the CCP4 molecular-graphics project Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 2004 2288 2294 (Pubitemid 41742782)
32. J.V. Silverton Origin 2.0 - scientific graphics and data analysis in Windows J. Am. Chem. Soc. 115 1993 3396